Predictive modeling of bovine respiratory disease outcomes in feedlot cattle: A narrative review

Bovine respiratory disease (BRD) is an ongoing health and economic challenge in the dairy and beef cattle industries. Multiple risk factors make an animal susceptible to BRD. The presence of Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis in lung tissues have been associated with BRD mortalities, but they are also commonly present in the upper respiratory tract of healthy animals. This study aims to compare the cattle nasal microbiome (diversity, composition and community interaction) and the abundance of BRD pathogens (by qPCR) in the nasal microbiome of Holstein steers that are apparently healthy (Healthy group, n = 75) or with BRD clinical signs (BRD group, n = 58). We then used random forest models based on nasal microbial community and qPCR results to classify healthy and BRD-affected animals and determined the agreement with the visual clinical signs. Additionally, co-occurring species pairs were identified in visually BRD or healthy animal groups.Cattle in the BRD group had lower alpha diversity than pen-mates in the healthy group. Amplicon sequence variants (ASVs) from Trueperella pyogenes, Bibersteinia and Mycoplasma spp. were increased in relative abundance in the BRD group, while ASVs from Mycoplasma bovirhinis and Clostridium sensu stricto were increased in the healthy group. Prevalence of H. somni (98%) and P. multocida (97%) was high regardless of BRD clinical signs whereas M. haemolytica (81 and 61%, respectively) and M. bovis (74 and 51%, respectively) were more prevalent in the BRD group than the healthy group. In the BRD group, the abundance of M. haemolytica and M. bovis was increased, while H. somni abundance was decreased. Visual observation of clinical signs agreed with classification by the nasal microbial community (misclassification rate of 32%) and qPCR results (misclassification rate 34%). Co-occurrence analysis demonstrated that the nasal microbiome of BRD-affected cattle presented fewer bacterial associations than healthy cattle.This study offers insight into the prevalence and abundance of BRD pathogens and the differences in the nasal microbiome between healthy and BRD animals. This suggests that nasal bacterial communities provide a potential platform for future studies and potential pen-side diagnostic testing. 

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Identification of bovine respiratory disease through the nasal microbiome

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Increasing evidence from human and other animal species supports the existence of a commensal microbiota in semen and that this seminal microbiota may influence not only sperm quality and fertility but also female reproduction. Seminal microbiota in bulls and its evolution and factors shaping this community, however, remain largely underexplored. ABSTRACT In this study, we evaluated the seminal and fecal microbiota in yearling beef bulls fed a common diet to achieve moderate (1.13 kg/day) or high (1.80 kg/day) rates of weight gain. Semen samples were collected on days 0 and 112 of dietary intervention (n = 19/group) as well as postbreeding (n = 6/group) using electroejaculation, and the microbiota was assessed using 16S rRNA gene sequencing, quantitative PCR (qPCR), and culturing. The fecal microbiota was also evaluated, and its similarity with seminal microbiota was assessed. A subset of seminal bacterial isolates (n = 33) was screened for resistance against 28 antibiotics. A complex and dynamic microbiota was detected in bovine semen, and the community structure was affected by sampling time (R2 = 0.16, P < 0.001). Microbial richness increased significantly from day 0 to day 112, and diversity increased after breeding (P > 0.05). Seminal microbiota remained unaffected by the differential rates of gain, and its overall composition was distinct from fecal microbiota, with only 6% of the taxa shared between them. A total of 364 isolates from 49 different genera were recovered under aerobic and anaerobic culturing. Among these seminal isolates were pathogenic species and those resistant to several antibiotics. Overall, our results suggest that bovine semen harbors a rich and complex microbiota which changes over time and during the breeding season but appears to be resilient to differential gains achieved via a common diet. Seminal microbiota is distinct from the fecal microbiota and harbors potentially pathogenic and antibiotic-resistant bacterial species. IMPORTANCE Increasing evidence from human and other animal species supports the existence of a commensal microbiota in semen and that this seminal microbiota may influence not only sperm quality and fertility but also female reproduction. Seminal microbiota in bulls and its evolution and factors shaping this community, however, remain largely underexplored. In this study, we characterized the seminal microbiota of yearling beef bulls and its response to the bull age, different weight gains, and mating activity. We compared bacterial composition between seminal and fecal microbiota and evaluated the diversity of culturable seminal bacteria and their antimicrobial resistance. Our results obtained from sequencing, culturing, and antibiotic susceptibility testing provide novel information on the taxonomic composition, evolution, and factors shaping the seminal microbiota of yearling beef bulls. This information will serve as an important basis for further understanding of the seminal microbiome and its involvement in reproductive health and fertility in cattle.

https://doi.org/10.1128/spectrum.05180-22

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain

Experimental bovine respiratory syncytial virus (BRSV) infection can enhance Histophilus somni (Hs) disease in calves; we thus hypothesized that modified-live virus (MLV) vaccines containing BRSV may alter Hs carriage. Our objective was to determine effects of an intranasal (IN) trivalent (infectious bovine rhinotracheitis virus [IBRV], parainfluenza-3 virus [PI3V], and BRSV) respiratory vaccine with parenteral (PT) bivalent bovine viral diarrhea virus (BVDV) type I + II vaccine, or a PT pentavalent (BVDV type I and II, IBRV, BRSV, and PI3V) respiratory vaccine, on health, growth, immunity, and nasal pathogen colonization in high-risk beef calves. Calves (n=525) were received in 5 truckload blocks and stratified by body weight (213±18.4 kg), sex, and presence of a pre-existing ear-tag. Pens were spatially arranged in sets of 3 within block and randomly assigned to treatment with an empty pen between treatment groups consisting of: 1) no MLV respiratory vaccination (CON), 2) IN trivalent MLV respiratory vaccine with PT BVDV type I + II vaccine (INT), or 3) PT pentavalent, MLV respiratory vaccine (INJ). Pen was the experimental unit, with 15 pens/treatment and 11 - 12 calves/pen in this 70-d receiving study. Health, performance, and BRSV, Hs, Mycoplasma bovis (Mb), Mannheimia haemolytica (Mh), and Pasteurella multocida (Pm) level in nasal swabs via rtPCR was determined on d 0, 7, 14, and 28, and BRSV-specific serum neutralizing antibody titer, and serum IFN-γ concentration via ELISA, were evaluated on d 0, 14, 28, 42, 56, and 70. Morbidity (P=0.83), mortality (P=0.68) and average daily gain (P≥0.82) did not differ. Serum antibody against BRSV increased with time (P<0.01). There was a treatment × time interaction (P<0.01) for Hs detection; on d 14 and 28, INT (21.1 and 57.1%) were more frequently (P<0.01) Hs positive than CON (3.6 and 25.3%) or INJ (3.4 and 8.4%). Also, INT had reduced (P=0.03) cycle time of Hs positive samples on d 28. No difference (P≥0.17) was found for IFN-γ concentration and Mb, Mh, or Pm detection. The proportion of Mh positive culture from lung specimens differed (P<0.01); INT had fewer (0.0%; 0 of 9) Mh positive lungs than INJ (45.5%; 6 of 13) or CON (74.0%; 14 of 19). Vaccination of high-risk calves with MLV did not clearly impact health or growth during the receiving period. However, INT was associated with altered upper respiratory microbial community in cattle resulting in increased detection and level of Hs.

Clinical and Microbiological effects in High-risk Beef Calves Administered Intranasal or Parenteral Modified-live Virus Vaccines.

OBJECTIVE To assess antibiotic use and other factors associated with death rates in beef feedlots in 3 regions of the US over a 10-year period. SAMPLE Data for 186,297 lots (groups) of finished cattle marketed between 2010 and 2019 were obtained from a database representing feedlots in the central, high, and north plains of the US. PROCEDURES Descriptive statistics were generated. Generalized linear mixed models were used to estimate lot death rates for each region, sex (steer or heifer), and cattle origin (Mexico or the US) combination. Death rate was calculated as the (number of deaths/number of cattle placed in the lot) × 100. Lot antibiotic use (TotalActiveMG/KGOut) was calculated as the total milligrams of active antibiotics assigned to the lot per live weight (in kilograms) of cattle marketed from the lot. Rate ratios were calculated to evaluate the respective associations between lot death rate and characteristics of cattle and antibiotic use. RESULTS Mean death rate increased during the 10-year period, peaking in 2018. Mean number of days on feed also increased over time. Mean TotalActiveMG/KGOut was greatest in 2014 and 2015, lowest in 2017, and moderated in 2018 and 2019. Death rate was positively associated with the number of days on feed and had a nonlinear association with TotalActiveMG/KGOut. Feeding medicated feed articles mitigated death rate. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested a balance between disease prevention and control in feedlots for cattle with various risk profiles. Additional data sources are needed to assess TotalActiveMG/KGOut across the cattle lifetime.

Population-level analysis of antibiotic use and death rates in beef feedlots over ten years in three cattle-feeding regions of the United States.

Feedlot closeout records from January 2005 through September 2014 were summarized. A total of 484,193 lots involving 73,067,534 cattle were used to illustrate mortality. Mortality rate and average days-on-feed at death by placement weight, sex, and cause of death (respiratory, digestive, and acute interstitial pneumonia) were calculated from these records. Mortality averaged 1.56 and 1.43% in heifers and steers, respectively. Mortality trends were seasonal; respiratory mortality was highest in late fall and early winter, digestive mortality was highest in late spring, and AIP mortality was greatest during summer months. Mortality during the first 30 days of the feeding period averaged 0.40% and 0.35% for heifers and steers, respectively. Mortality in the mid-portion of the feeding period, the last 31 to 60 days, and the last 30 days of feed averaged 0.70%, 0.20%, and 0.26% for heifers and 0.70%, 0.18%, and 0.21% for steers, respectively. These data suggest animal mortality is not isolated to the receiving period and occurs at comparable rates thereafter.

Jason L. Bargen

Papers

Population-level analysis of antibiotic use and death rates in beef feedlots over ten years in three cattle-feeding regions of the United States.

A Retrospective evaluation of animal mortality in US feedlots